Special

MmuINT0151699 @ mm9

Intron Retention

Gene
ENSMUSG00000057738 | Spna2
Description
spectrin alpha 2 [Source:MGI Symbol;Acc:MGI:98386]
Coordinates
chr2:29849320-29849885:+
Coord C1 exon
chr2:29849320-29849475
Coord A exon
chr2:29849476-29849680
Coord C2 exon
chr2:29849681-29849885
Length
205 bp
Sequences
Splice sites
5' ss Seq
AAAGTAATA
5' ss Score
0.92
3' ss Seq
CTTCTTTTTTTGATTCGCAGGAT
3' ss Score
9.68
Exon sequences
Seq C1 exon
CTCCTGAGCCGCCGCAATGCCCTTCATGAGCGAGCCATGCATCGCCGGGCACAGCTGGCTGATTCCTTCCATCTGCAGCAGTTCTTCCGTGATTCTGATGAGCTCAAAAGTTGGGTCAACGAGAAGATGAAAACGGCCACCGATGAAGCTTATAAA
Seq A exon
GTAATAAAATCAGAGTTTCCTTTAGTAGTTGTGTAGTAAGCTAAACCTTGCAAAAACTACTTGGAGCTAAAAAAACAAAACCAAAAAACACAAAGAAGGTCACACAAACCACACTAGTTAGCGTAAATCTTCTGTTTTATGAGTGTGAAGTAGCTATATATATTCTCCAGTTCAGGCACAACCCTCTTCTTTTTTTGATTCGCAG
Seq C2 exon
GATCCATCCAACCTGCAAGGGAAAGTCCAAAAGCATCAGGCTTTTGAGGCTGAGCTTTCAGCAAACCAGAGCCGGATTGATGCCCTTGAGAAAGCTGGGCAGAAGCTAATAGATGTCAACCACTATGCCAAGGAAGAAGTAGCAGCTCGTATGAATGAGGTCATCAGTTTGTGGAAGAAACTTCTAGAGGCCACAGAACTGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057738-Spna2:NM_001076554:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.135 A=NA C2=0.159
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0043516=Spectrin=PD(19.0=38.5),PF0043516=Spectrin=PU(27.9=55.8)

							
A:
NA

							
C2:
PF0043516=Spectrin=FE(65.4=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000109348





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000047792, ENSMUSP00000092697, ENSMUSP00000097797, ENSMUSP00000109346
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr9:131345129-131345355 
LOW PSI
HsaINT0158364
(SPTAN1)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr11:99144289-99144506 
LOW PSI
BtaINT0140421
(SPTAN1)
Chicken
(galGal4)
chr17:5156933-5157259 
LOW PSI
GgaINT0124356
(SPTAN1)
Chicken
(galGal3)
chr17:5783745-5784071 
LOW PSI
GgaINT0124356
(SPTAN1)
Zebrafish
(danRer10)
chr21:13075294-13075444 
LOW PSI
DreINT0155163
(spna2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TTCATGAGCGAGCCATGCATC

				
R: 
TGACCTCATTCATACGAGCTGC

				
Band lengths: 
297-502

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Pre-implantation embryo development
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






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